:: DESCRIPTION
E-TALEN is a software tool to design and evaluate Transcription Activator Like Effector Nucleases (TALEN)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2013 Nov 1;41(20):e190. doi: 10.1093/nar/gkt789.
E-TALEN: a web tool to design TALENs for genome engineering.
Heigwer F, Kerr G, Walther N, Glaeser K, Pelz O, Breinig M, Boutros M.
:: DESCRIPTION
southern_blot_design is a novel software pipeline for designing and optimizing Southern blot probes in silico for use against genomic DNA targets.
::DEVELOPER
Genes to Cognition (G2C)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2010 Jan 29;11:74. doi: 10.1186/1471-2164-11-74.
Automated design of genomic Southern blot probes.
Croning MD1, Fricker DG, Komiyama NH, Grant SG.
:: DESCRIPTION
pVACtools is a computational toolkit for aiding design of personalized cancer vaccines.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hundal, Kiwala et al. 2020.
pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens.
Cancer Immunology Research. 8(3):409-420.
:: DESCRIPTION
D2CMA contains a few R-scripts, mainly the function optimize.MA.design which builds upon the daMA package. It was used to optimize the two-color microarray experimental design for analyzing the differential responses of sensitive and tolerant rice cultivars to drought stress
::DEVELOPER
Max Planck Institute for Molecular Plant Physiology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
OligoWiz performs intelligent design of oligonucleotides for DNA microarrays. It is implemented as a client-server solution, which consist of an easy to use Graphical User Interface (written in Java) which delegates the computationally intensive operations to a powerful Multi-CPU server hosted at the Center for Biological Sequence Analysis.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
OligoWiz 2.0 – integrating sequence feature annotation into design of microarray probes
Rasmus Wernersson and Henrik Bjørn Nielsen.
Nucleic Acids Research, 2005, Vol. 33, Web Server issue W611-W615
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.
Henrik Bjørn Nielsen, Rasmus Wernersson and Steen Knudsen.
Nucleic Acids Research, 2003, Vol. 31, No. 13 3491-3496
:: DESCRIPTION
MODEST allows the rapid and effective design of optimal MAGE (multiplex automated genome engineering) oligos based on simple input, to achieve any mutation possible with MAGE.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.
Bonde MT, Klausen MS, Anderson MV, Wallin AI, Wang HH, Sommer MO.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W408-15. doi: 10.1093/nar/gku428
:: DESCRIPTION
CellBlender is an addon for Blender-2.6x to create computational cell biology models for use in MCell and potentially other cell simulation biophysics engines. In CellBlender 0.49 you can create geometric objects, assign surface regions to said objects, export the objects as MCell MDL geometry files, set MCell simulation parameters, import a time-series of MCell VIZ_OUTPUT, and interactively playback or render an animation of the VIZ_OUTPUT. MDL import along with other features will be added in future versions.
CellBlender is replacing PSC_DX and DReAMM as the primary tool to visualize MCell simulations.
::DEVELOPER
The National Center for Multiscale Modeling of Biological Systems (MMBioS)
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Stiles, JR, and Bartol, TM. (2001).
Monte Carlo methods for simulating realistic synaptic microphysiology using MCell.
In: Computational Neuroscience: Realistic Modeling for Experimentalists, ed. De Schutter, E. CRC Press, Boca Raton, pp. 87-127.
:: DESCRIPTION
BioJazz is a tool for evolving and designing biochemical reaction networks using genetic algorithm (GA).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.
Feng S, Ollivier JF, Swain PS, Soyer OS.
Nucleic Acids Res. 2015 Jun 22. pii: gkv595.
:: DESCRIPTION
STAMP is a Staden package extension for automating microsatellite marker design. It integrates the de novo repeat identification program Phobos by Christoph Mayer and PRIMER3 into Pregap and Gap4. It allows tagging repeats for masking them out for assembly (Pregap), finding repeats in assembled Gap4 databases, automatic primer design flanking marked repeats and multiplex primer design.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K. & Frickenhaus, S (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.
:: DESCRIPTION
HYDEN (HighlY DEgeNerate primers) is a program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp).
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Degenerate primer design: theoretical analysis and the HYDEN program.
Linhart C, Shamir R.
Methods Mol Biol. 2007;402:221-44.
